CUX2.H12INVIVO.2.S.C motif - HOmo sapiens COmprehensive MOdel COllection

Motif	CUX2.H12INVIVO.2.S.C
Gene (human)	CUX2 (GeneCards)
Gene synonyms (human)	CUTL2, KIAA0293
Gene (mouse)	Cux2
Gene synonyms (mouse)	Cutl2
LOGO
LOGO (reverse complement)
Motif subtype	2
Quality	C

Motif length	13
Consensus	hdRKTGATCASnn
GC content	43.01%
Information content (bits; total / per base)	12.566 / 0.967
Data sources	HT-SELEX
Aligned words	8253

ChIP-Seq benchmarking	Num. of experiments (peaksets)	auROC, median	auROC, best	auPRC, median	auPRC, best	pseudo-auROC, median	pseudo-auROC, best	pseudo-log-auROC, median	pseudo-log-auROC, best	Centrality, median	Centrality, best
Mouse	1 (5)	0.804	0.82	0.703	0.726	0.636	0.664	1.702	1.831	128.066	160.495

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.966	0.95	0.867	0.854	0.696	0.723
Overall, 4 experiments	best	0.992	0.988	0.985	0.977	0.966	0.954
Methyl HT-SELEX, 1 experiments	median	0.99	0.986	0.901	0.896	0.711	0.747
Methyl HT-SELEX, 1 experiments	best	0.99	0.986	0.901	0.896	0.711	0.747
Non-Methyl HT-SELEX, 3 experiments	median	0.942	0.915	0.833	0.813	0.682	0.698
Non-Methyl HT-SELEX, 3 experiments	best	0.992	0.988	0.985	0.977	0.966	0.954

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.82	0.404	0.727	0.487

TF superclass	Helix-turn-helix domains {3} (TFClass)
TF class	Homeo domain factors {3.1} (TFClass)
TF family	HD-CUT {3.1.9} (TFClass)
TF subfamily	CUX {3.1.9.2} (TFClass)
TFClass ID	TFClass: 3.1.9.2.2
HGNC	HGNC:19347
MGI	MGI:107321
EntrezGene (human)	GeneID:23316 (SSTAR profile)
EntrezGene (mouse)	GeneID:13048 (SSTAR profile)
UniProt ID (human)	CUX2_HUMAN
UniProt ID (mouse)	CUX2_MOUSE
UniProt AC (human)	O14529 (TFClass)
UniProt AC (mouse)	P70298 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 1 mouse
HT-SELEX	3
Methyl-HT-SELEX	1

PCM	CUX2.H12INVIVO.2.S.C.pcm
PWM	CUX2.H12INVIVO.2.S.C.pwm
PFM	CUX2.H12INVIVO.2.S.C.pfm
Alignment	CUX2.H12INVIVO.2.S.C.words.tsv
Threshold to P-value map	CUX2.H12INVIVO.2.S.C.thr
Motif in other formats
JASPAR format	CUX2.H12INVIVO.2.S.C_jaspar_format.txt
MEME format	CUX2.H12INVIVO.2.S.C_meme_format.meme
Transfac format	CUX2.H12INVIVO.2.S.C_transfac_format.txt
Homer format	CUX2.H12INVIVO.2.S.C_homer_format_0.001.txt CUX2.H12INVIVO.2.S.C_homer_format_0.0005.txt CUX2.H12INVIVO.2.S.C_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1526.75	2427.75	1205.75	3092.75
02	3581.75	594.75	2250.75	1825.75
03	6128.0	334.0	1443.0	348.0
04	2.0	1197.0	1277.0	5777.0
05	2.0	3686.0	2.0	4563.0
06	0.0	0.0	8253.0	0.0
07	8253.0	0.0	0.0	0.0
08	0.0	1.0	0.0	8252.0
09	10.0	7004.0	0.0	1239.0
10	6324.0	1.0	1925.0	3.0
11	591.0	1102.0	6257.0	303.0
12	1194.0	2277.0	1755.0	3027.0
13	2300.5	1272.5	1875.5	2804.5

PFM

	A	C	G	T
01	0.185	0.294	0.146	0.375
02	0.434	0.072	0.273	0.221
03	0.743	0.04	0.175	0.042
04	0.0	0.145	0.155	0.7
05	0.0	0.447	0.0	0.553
06	0.0	0.0	1.0	0.0
07	1.0	0.0	0.0	0.0
08	0.0	0.0	0.0	1.0
09	0.001	0.849	0.0	0.15
10	0.766	0.0	0.233	0.0
11	0.072	0.134	0.758	0.037
12	0.145	0.276	0.213	0.367
13	0.279	0.154	0.227	0.34

PWM

	A	C	G	T
01	-0.301	0.163	-0.536	0.404
02	0.551	-1.241	0.087	-0.122
03	1.088	-1.815	-0.357	-1.774
04	-6.185	-0.544	-0.479	1.029
05	-6.185	0.58	-6.185	0.793
06	-6.82	-6.82	1.385	-6.82
07	1.385	-6.82	-6.82	-6.82
08	-6.82	-6.453	-6.82	1.385
09	-5.127	1.221	-6.82	-0.509
10	1.119	-6.453	-0.069	-5.974
11	-1.248	-0.626	1.109	-1.912
12	-0.546	0.098	-0.162	0.383
13	0.109	-0.483	-0.095	0.307

Standard thresholds

P-value	Threshold
0.001	3.019965
0.0005	4.89201
0.0001	7.477135